I don't have a Python solution (something I'd love to see), but I have used the GeoHMS command without having to go through the whole processing of generating a GeoHMS project. You can simply start with the Arc Hydro process and then set up the layers in the Data Management portion of the GeoHMS toolbar and then use the toolbar menus. I do this for the parameter menu also. The latest GeoHMS actually has the terrain processing commands built into the GeoHMS toolbar. So, you can do almost all of the terrain processing and all using the GeoHMS toolbar.